+Open data
-Basic information
Entry | Database: PDB / ID: 1zvj | ||||||
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Title | Structure of Kumamolisin-AS mutant, D164N | ||||||
Components | kumamolisin-As | ||||||
Keywords | HYDROLASE / D164N / Kumamolisin-As | ||||||
Function / homology | Function and homology information tripeptidyl-peptidase activity / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Alicyclobacillus sendaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 2.03 Å | ||||||
Authors | Li, M. / Wlodawer, A. / Gustchina, A. / Nakayama, T. | ||||||
Citation | Journal: Febs J. / Year: 2006 Title: Processing, catalytic activity and crystal structures of kumamolisin-As with an engineered active site. Authors: Okubo, A. / Li, M. / Ashida, M. / Oyama, H. / Gustchina, A. / Oda, K. / Dunn, B.M. / Wlodawer, A. / Nakayama, T. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity. Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Tsuruoka, N. / Ashida, M. / Minakata, H. / Oyama, H. / Oda, K. / Nishino, T. / Nakayama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zvj.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zvj.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zvj_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
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Full document | 1zvj_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 1zvj_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1zvj_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/1zvj ftp://data.pdbj.org/pub/pdb/validation_reports/zv/1zvj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36717.371 Da / Num. of mol.: 1 / Mutation: D164N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus sendaiensis (bacteria) Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GB88 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.42 Å3/Da / Density % sol: 39.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: PEG8000, Ammounium Sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: Osmic |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. all: 17485 / Num. obs: 17485 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rsym value: 0.044 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 1450 / Rsym value: 0.143 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 2.03→10 Å / Num. parameters: 10987 / Num. restraintsaints: 10622 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2742.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→10 Å
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Refine LS restraints |
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